generating code:
Bac.rank.names<-rank_names(Bac)[2:6]
# add this line to beginning
# cat('\n # Set min plotting threshold to 0.5% relative abundance (all-sample a.k.a global mean) \n')
#also adding psmelt step
for(rank in Bac.rank.names) {
cat('\n## \n')
cat('################## \n')
cat('# Bac:', rank, '# \n')
cat('################## \n')
cat('\n')
cat('min_nname_Bac_', rank, '<-length(unique(Bac_', rank, '_Mean_Abund$',
rank, '[Bac_', rank, '_Mean_Abund$Bac_', rank, '_Mean > 0.5]))',
sep = '')
cat('\n \n ')
cat('if (min_nname_Bac_', rank, ' < 10){
Bac.', rank, '.names.to.plot<-top_n(Bac_', rank, '_Mean_Abund, min_nname_Bac_', rank, ', Bac_', rank, '_Mean)$',rank, '
} else {
Bac.', rank, '.names.to.plot<-top_n(Bac_', rank, '_Mean_Abund, 10, Bac_', rank, '_Mean)$', rank, '
}', sep = '')
cat('\n# \n')
cat('\nBac.',rank,'.A <- tax_glom(Bac, taxrank="',rank,'")\n',sep = '')
cat('Bac.',rank,' <- prune_taxa(taxa_sums(Bac.',rank,'.A) > 0, Bac.',rank,'.A)\n',sep = '')
cat('Bac.',rank,'.r = transform_sample_counts(Bac.',rank,', function(x) x / sum(x) )\n',sep = '')
cat('dat_Bac.',rank,'.r <- psmelt(Bac.',rank,'.r)\n',sep = '')
cat('dat_Bac.',rank,'.r$',rank,' <- as.character(dat_Bac.',rank,'.r$',rank,') \n',sep = '')
cat('dat_Bac.',rank,'.r$',rank,'_all <- dat_Bac.',rank,'.r$',rank,' \n',sep = '')
cat('dat_Bac.',rank,'.r$',rank,' <- if_else(dat_Bac.',rank,'.r$',rank,' %in% Bac.',rank,'.names.to.plot, dat_Bac.',rank,'.r$',rank,', "LowAbundance") \n',sep = '')
cat('\n## \n')
cat('\n \n')
}
Fun.rank.names<-rank_names(Fun)[2:7] #change 6 to 7 if fungal
# add this line to beginning
# cat('\n # Set min plotting threshold to 0.5% relative abundance (all-sample a.k.a global mean) \n')
#also adding psmelt step
for(rank in Fun.rank.names) {
cat('\n## \n')
cat('################## \n')
cat('# Fun:', rank, '# \n')
cat('################## \n')
cat('\n')
cat('min_nname_Fun_', rank, '<-length(unique(Fun_', rank, '_Mean_Abund$',
rank, '[Fun_', rank, '_Mean_Abund$Fun_', rank, '_Mean > 0.5]))',
sep = '')
cat('\n \n ')
cat('if (min_nname_Fun_', rank, ' < 10){
Fun.', rank, '.names.to.plot<-top_n(Fun_', rank, '_Mean_Abund, min_nname_Fun_', rank, ', Fun_', rank, '_Mean)$',rank, '
} else {
Fun.', rank, '.names.to.plot<-top_n(Fun_', rank, '_Mean_Abund, 10, Fun_', rank, '_Mean)$', rank, '
}', sep = '')
cat('\n# \n')
cat('\nFun.',rank,'.A <- tax_glom(Fun, taxrank="',rank,'")\n',sep = '')
cat('Fun.',rank,' <- prune_taxa(taxa_sums(Fun.',rank,'.A) > 0, Fun.',rank,'.A)\n',sep = '')
cat('Fun.',rank,'.r = transform_sample_counts(Fun.',rank,', function(x) x / sum(x) )\n',sep = '')
cat('dat_Fun.',rank,'.r <- psmelt(Fun.',rank,'.r)\n',sep = '')
cat('dat_Fun.',rank,'.r$',rank,' <- as.character(dat_Fun.',rank,'.r$',rank,') \n',sep = '')
cat('dat_Fun.',rank,'.r$',rank,'_all <- dat_Fun.',rank,'.r$',rank,' \n',sep = '')
cat('dat_Fun.',rank,'.r$',rank,' <- if_else(dat_Fun.',rank,'.r$',rank,' %in% Fun.',rank,'.names.to.plot, dat_Fun.',rank,'.r$',rank,', "LowAbundance") \n',sep = '')
cat('\n## \n')
cat('\n \n')
}